Variant report

Variant	rs11171794
Chromosome Location	chr12:39739943-39739944
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39738067..39741527-chr12:39743955..39747329,3	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11171568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171662	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11171666	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171669	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11171682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11171691	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11171732	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171797	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171834	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171844	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11171940	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171955	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11172109	0.92[AFR][1000 genomes]
rs11172168	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs11172263	0.81[EUR][1000 genomes]
rs11172373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12227642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[ASN][1000 genomes]
rs12228664	0.81[EUR][1000 genomes]
rs12231250	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12231735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17127059	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs17127072	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs17127115	0.92[AFR][1000 genomes]
rs17127119	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs3923944	1.00[YRI][hapmap]
rs56154721	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326136	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56885420	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57785083	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58125663	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58648215	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61101304	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61453715	0.92[AFR][1000 genomes]
rs7964039	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv558590	chr12:39724344-39751273	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39695600-39742000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:39696600-39762200	Weak transcription	Fetal Brain Male	brain
3	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
4	chr12:39699600-39760600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:39704200-39746200	Weak transcription	HUVEC	blood vessel
6	chr12:39715600-39741800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:39718400-39756800	Weak transcription	HSMM	muscle
8	chr12:39721000-39770600	Weak transcription	Gastric	stomach
9	chr12:39721600-39752400	Weak transcription	Right Ventricle	heart
10	chr12:39722800-39767200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:39724400-39751800	Weak transcription	Fetal Heart	heart
12	chr12:39725000-39750000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr12:39725200-39753600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:39725800-39749800	Weak transcription	K562	blood
15	chr12:39726000-39753800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:39726400-39749800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:39726400-39766600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr12:39726600-39766600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:39726600-39766600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:39726600-39766800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:39726800-39740200	Weak transcription	Brain Substantia Nigra	brain
22	chr12:39726800-39749800	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:39726800-39762200	Weak transcription	Placenta	Placenta
24	chr12:39726800-39766600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr12:39727000-39749000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:39727000-39749400	Weak transcription	Adipose Nuclei	Adipose
27	chr12:39727000-39749800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:39727000-39750000	Weak transcription	Brain Anterior Caudate	brain
29	chr12:39727000-39750000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:39727000-39751000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr12:39727000-39751800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:39727000-39753800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:39727000-39755400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:39727000-39755600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:39727000-39758000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:39727000-39758000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr12:39727000-39758200	Weak transcription	Fetal Intestine Large	intestine
38	chr12:39727000-39760600	Weak transcription	Brain Angular Gyrus	brain
39	chr12:39727000-39761400	Weak transcription	Fetal Intestine Small	intestine
40	chr12:39727000-39762400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr12:39727000-39767000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
43	chr12:39727200-39749800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr12:39728800-39750200	Weak transcription	Hela-S3	cervix
45	chr12:39733000-39750000	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:39733600-39749200	Weak transcription	Fetal Brain Female	brain
47	chr12:39734600-39749000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:39734800-39742200	Weak transcription	Brain Germinal Matrix	brain
49	chr12:39735200-39761400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr12:39735600-39741600	Weak transcription	Liver	Liver

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